User: brianna.flynn

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Posts by brianna.flynn

<prev • 6 results • page 1 of 1 • next >
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Answer: A: plink list-duplicate-vars not working
... Hi Cynthia, I've been having the same problem with plink lately! I think if you can't get plink to work, you can remove the duplicates from the bim file yourself by writing another script in bash or python. Here are some bash scripts I've used lately to check for dupes: sort -u your-file.bim ...
written 4 months ago by brianna.flynn10
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Comment: C: How to obtain a novel virus' complete genome from de novo assembly
... Hey Mensur, I didn't clarify this in the parent post but we did find other viral contigs (known bee, insect and plant viruses ) - the one viral contig I refer to the most is the one that we think is a new species. Thank you for the suggestions! I'll look into using PLASS ...
written 10 months ago by brianna.flynn10
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Comment: C: How to obtain a novel virus' complete genome from de novo assembly
... Yes, we expect to find bee host RNA, plant RNA and RNA viruses (typically from pollen, though some plant viruses do infect bee hosts), and insect specific RNA viruses. ...
written 10 months ago by brianna.flynn10
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How to obtain a novel virus' complete genome from de novo assembly
... Hello all, I have a viral genomics question for you! I am analyzing an RNA-Seq library comprised of pooled RNA samples from bumble bees across the United States, in order to quantify the diversity of viruses that infect these populations. I assembled the RNA-Seq reads into contigs using the *de no ...
assembly rna-seq virus written 10 months ago by brianna.flynn10 • updated 10 months ago by Mensur Dlakic7.1k
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Answer: A: Getting scientific name (ssciname) in Blastn output
... Hi Amar! I finally got it to work for me by downloading the accession2taxid file from the NCBI FTP site, and then creating a new blast database with the taxids using the option `-taxid_map` following this post: https://www.biostars.org/p/76551/ ...
written 12 months ago by brianna.flynn10
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Getting scientific name (ssciname) in Blastn output
... Hey all, I would like to get the scientific names of each of my blast hits from blastn run locally. I have downloaded the taxdb.tar.gz taxonomy database from NCBI and have set the $BLASTDB variable to the directory with my blast database and query contigs. In my tabbed output, all I get is an 'N/A ...
alignment blast written 12 months ago by brianna.flynn10

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